Microbial Diversity Lecture Notes PDF

Microbial Diversity Introduction Microorganisms were the first cellular life forms and were active more than 3 billion years prior to the appearance of macroorganisms. The study of microbial diversity began with the discovery of microorganisms by Antonie van Leeuwenhoek in the 17th century. A...

Microbial Diversity Introduction Microorganisms were the first cellular life forms and were active more than 3 billion years prior to the appearance of macroorganisms. The study of microbial diversity began with the discovery of microorganisms by Antonie van Leeuwenhoek in the 17th century. Advancements in microscopy, culturing techniques, and molecular biology have since expanded our understanding of the diversity and roles of microbes in nature. The immense diversity, small size, and clonal nature of most microorganisms explain why quantifying the biodiversity of microorganisms is fundamentally different from quantifying that of macroorganisms. Microbial diversity is defined as the variety of microorganisms found in different environments, ranging from soil and water to extreme habitats like hot springs and deep-sea vents. This diversity is not just about the number of species but also includes genetic diversity within species, as well as the variety of metabolic and ecological roles that microbes play. The microorganisms found in the environment are generally thought to consist of: Bacteria (including actinomycetes); Archaea; Fungi; Protozoa; Algae; and Viruses. Microbial diversity is crucial for maintaining the health of ecosystems, contributing to nutrient cycling, and supporting life on Earth. Importance of Microbial Diversity: 1. Ecological Stability: Microbial diversity ensures the stability and resilience of ecosystems by contributing to biogeochemical cycles, including carbon, nitrogen, and sulfur cycles. Microbes are crucial in processes such as decomposition, nitrogen fixation, and photosynthesis, which are fundamental for life on Earth. 2. Human Health: The human microbiome, which consists of trillions of microbes living in and on our bodies, is essential for our health. It aids in digestion, produces essential vitamins, protects against pathogens, and modulates the immune system. A diverse microbiome is associated with better health outcomes, while a loss of microbial diversity is linked to diseases such as obesity, allergies, and autoimmune disorders. 3. Biotechnology and Industry: Microbial diversity is a treasure trove for biotechnology. Microorganisms are used in the production of antibiotics, enzymes, 1 biofuels, and fermented foods. The discovery of new microbes and their unique metabolic pathways can lead to innovations in medicine, agriculture, and environmental management. 4. Environmental Monitoring and Bioremediation: Microbes are sensitive indicators of environmental changes. Monitoring shifts in microbial communities can provide early warnings of environmental disturbances such as pollution or climate change. Additionally, certain microbes can degrade pollutants, making them valuable in bioremediation efforts to clean up contaminated environments. 5. Evolutionary Insights: Studying microbial diversity provides insights into the evolutionary history of life on Earth. Microbes were the first forms of life, and their evolutionary adaptations have shaped the planet's atmosphere and ecosystems. Understanding microbial evolution can also inform the search for life on other planets. Classification of organisms Until the 1970s, classification ion of macro- and microorganisms was based primarily on physiological differences with anywhere from two to six major kingdoms proposed for categorizing life as we know it. However, in the 1970s techniques became available to allow examination of nucleic acids, including ribosomal RNA (rRNA). In the 1980's, Woese began phylogenetic analysis of all forms of cellular life based on comparative sequencing of the small subunit ribosomal RNA (ssrRNA) that is contained in all organisms. Based on analysis of 16S rRNA, Carl Woese identified an entirely new group of organisms, the Archaea which eventually led to the modern classification of living organisms into a three-domain system consisting of Archaea, Eukarya and Bacteria (Fig.1). Of these, the Bacteria and Archaea are termed prokaryotes, and the Eukarya are known as eukaryotes. Within the Eukarya are fungi, protozoa, algae, plants, animals and humans. 2  Fig.1 The three-domain Tree of Life Although the definitive difference between Woese's Archaea and Bacteria is based on fundamental differences in the nucleotide base sequence in the 16S ribosomal RNA, there are many phenotypic and structural differences between the two groups of procaryotes 3  Viruses Viruses are still biologists’ puzzle because they show both living and non - living characters. Hence viruses are regarded as a separate entity. It is not considered in Whittaker’s five kingdom classification. Viruses are now defined as ultramicroscopic, disease causing intra cellular obligate parasites for bacteria plants and animals (infective agents) Table1: Different characters of Viruses Living characteristics of virus Non-living characteristics of virus Ability to multiply inside a host plant Inability to multiply extracellularly or animal cell Ability to cause diseases Absence of any metabolic activity Possession of nucleic acid, protein, Absence of protoplasm enzyme, etc. Ability to undergo mutation Can be crystallized. General characteristics They are very simple in their structure. They are composed of nucleic acid surrounded by a protein coat. Nucleic acid can be either RNA or DNA, but never both. They have no cellular organization and have no machinery for any metabolic activity. They are obligated to intracellular parasites, and they multiply within their host cells. Once outside the host cell they are completely inactive. An intact, infective virus particle which is non-replicating outside a host cell is called virion. They do not possess any ribosomes. Some viruses contain enzymes Geometrically fixed, they have a definite unchangeable shape, size and molecular weight (does not grow). 4 Size and Shape Viruses are very minute particles that can be seen only under electron microscope. Generally, they vary from 10 nm to 350 nm in size. Very small size and ability to pass through bacterial filters are classic attributes of viruses (Ultrafiltrable). Viruses are 10,000 times smaller than bacteria. The comparative sizes are illustrated in Fig.2 Fig.2 Different virus species are shown here to scale inside an E. coli bacterium Virus particle structure A mature virus particle is also known as a virion. It consists of either two or three basic components: A genome of DNA or RNA, but never both double-stranded or single- stranded, linear or circular, and in some cases segmented. A single-stranded nucleic acid can have plus or minus polarity. Fig.3 Viral genome 5  The capsid, the outer protein coat enclosing the nucleic acid of the virus and determining its antigenicity; the capsid can have a cubic (rotational), helical or complex symmetry and is made up of subunits called capsomers. The capsid is in close contact with nucleic acid and hence known as nucleocapsid. In some cases, an envelope that surrounds the capsid and is always derived from cellular membranes, they are called enveloped viruses. Others are called naked viruses or non- enveloped viruses Fig.4 Virus particle structure The infective nature of the virus is attributed to nucleic acid while host specificity is attributed to the protein coat. 6  Fig.5 Viral shapes Classification of virus Although viruses are not classified as members of the five kingdoms, they are diverse enough to require their own classification scheme to aid in their study and identification. According to the type of the host they infect, viruses are classified mainly into the following four types. 1. Plant viruses including algal viruses-RNA/DNA: e.g., Mosaic diseases of tobacco (TMV) 2.Animal viruses including human viruses-DNA/RNA, e.g., herpes, hepatitis A, B, C, influenza, AIDS and SARS. 3.Fungal viruses (Mycoviruses)-ds RNA 4.Bacterial viruses (Bacteriophages) including cyanophages 1- Bacteriophage Bacteriophages are viruses that infect bacteria. Also known as phages (coming from the root word ‘phagein’ meaning “to eat”), these viruses can be found everywhere bacteria exist including, in the soil, deep within the earth’s crust, inside plants and animals, and even in the oceans. The oceans hold some of the densest natural sources 7  of phages in the world. The structure of a bacteriophage is highly specialized to perform its function of infecting bacterial cells. The general structure of a bacteriophage can be described in terms of the following components: Head: Contains the viral nucleic acid (DNA or RNA) enclosed in a protein shell, often icosahedral. Tail: A hollow structure that helps inject the viral genome into the bacterial cell. Some phages have complex contractile tails (e.g., T4 phage), while others have simpler, non-contractile tails. Base Plate: Located at the end of the tail, helps in attaching to the bacterial surface. Tail Fibers: Aid in host recognition and attachment. Tail pins Tail fibers Fig.6 Bacteriophage structure Different types of bacteriophages About 96% of the reported bacteriophages belong to the Caudovirales order, which includes three families: Myoviridae that have contractile tail, Podoviridae that have short tail and Siphoviridae have non-contractile long tail as shown in Table 2 8 Table 2: Different types of bacteriophages Attachment/ Nucleic Order Family Examples Morphology Baseplate and tail acid fibers T4 Phage Linear ds Complex structure (Complex Nonenveloped, DNA allowing specific Caudovirales Myoviridae Bacteriophage) contractile tail attachment to the bacterial cell wall. T7, T3 Linear ds Complex structure Nonenveloped, DNA allowing specific Caudovirales Podoviridae short contractile attachment to the tail bacterial cell wall. Lambda Phage Nonenveloped, Linear ds Uses tail fibers for Caudovirales Siphoviridae (Temperate non-contractile DNA binding to bacterial Phage) long tail surface receptors. M13 Phage Circular Binds to specific (Filamentous Single- pili on the bacterial Nonenveloped, Tubulavirales Inoviridae Phage) stranded cell surface for filamentous DNA infection. (ssDNA) The main differences among bacteriophages lie in their tail structures (contractile vs. non-contractile), genome type (DNA vs. RNA), and modes of infecting bacterial cells. Fig. 7 Schematic representations of the main types of bacterial viruses. 9  2- Tobacco Mosaic Virus (TMV) Tobacco Mosaic Virus (TMV) is one of the most well-studied plant viruses and was the first virus ever discovered. It primarily infects tobacco plants and other members of the Solanaceae family, causing characteristic mosaic-like mottling of the leaves. TMV is a rod- shaped virus that measures approximately 300 nm in length and 18 nm in diameter. Capsid: The capsid is composed of approximately 2,130 identical protein subunits, known as coat proteins or capsomeres. These proteins are arranged in a helical pattern around the viral RNA. Viral RNA (Genetic Material): The genetic material of TMV is a single-stranded, positive-sense RNA (+ssRNA) molecule that is about 6,400 nucleotides long. This RNA molecule is tightly associated with the coat proteins, forming the helical core of the virus. Fig. 8 TMV structure 2- Animal Viruses a. Poxvirus: The smallpox virus or the variola virus is representative of the pox viruses, a group of agents that infect both humans and lower animals and produce characteristic vesicular skin lesions often called pocks. Pox viruses are the largest of animal viruses. They can be seen with phase optics or in stained preparation with the light microscope. Poxviruses are brick shaped. and have a complex internal structure including: Genome: Double-stranded DNA (dsDNA). a double-stranded DNA genome (130–260 kb) Capsid: Complex and lacks the typical icosahedral or helical symmetry seen in many viruses. 10  Envelope: Poxviruses have a double-layered membrane envelope derived from the host cell. Core: Contains a dumbbell-shaped core that houses the viral genome and associated proteins necessary for replication and transcription. Fig. 9 Pox virus b. Poliovirus, Poliomyelitis is a highly infectious viral disease that largely affects children under 5 years of age. The virus is transmitted by person-to-person spread mainly through the fecal-oral route or, less frequently, by a common vehicle (e.g. contaminated water or food) and multiplies in the intestine, from where it can invade the nervous system and cause paralysis.) Genome: Single-stranded RNA (ssRNA), positive-sense. Capsid: Icosahedral symmetry composed of 60 copies each of four coat proteins that protect the RNA. Fig. 10 Polio virus 11 c. Human Immunodeficiency Virus (HIV) Human immunodeficiency virus (HIV) is a virus that attacks the body’s immune system. Acquired immunodeficiency syndrome (AIDS) occurs at the most advanced stage of infection. HIV targets the body’s white blood cells, weakening the immune system. This makes it easier to get sick with diseases like tuberculosis, infections and some cancers. HIV is spread from the body fluids of an infected person, including blood, breast milk, semen and vaginal fluids. Genome: The HIV genome is composed of two identical single strands of positive-sense RNA. This RNA genome is about 9.7 kilobases long and contains nine genes that encode 15 different viral proteins Capsid: Includes a layer of a protein called p17 and an inner layer protein called p24 (conical or bullet- shaped). Encloses the viral RNA and enzymes necessary for reverse transcription (reverse transcriptase). Envelope: A lipid bilayer derived from the host cell membrane containing glycoproteins (gp120 and gp41), essential for binding to CD4 receptors on host cells. Enzymes: Contains reverse transcriptase, integrase, and protease for replication and integration into the host genome. Fig. 11 ADIS virus 12 Table 3: Difference between some animal viruses Feature Poxvirus Poliovirus ADIS Virus Family Poxviridae Picornaviridae Retroviridae Single-stranded Single-stranded RNA Genome Double-stranded DNA RNA (SSRNA), (SSRNA), positive- Type (dsDNA) positive-sense sense Yes, with lipid Yes, with lipid bilayer No, non- bilayer containing Envelope and surface proteins enveloped glycoproteins (gp120, gp41) Spherical or Shape Brick-shaped or ovoid Spherical icosahedral Complex with outer Enveloped, cone- envelope, surface shaped (capsid) Unique tubules, lateral bodies Non-enveloped Structural icosahedral Reverse Features Viral core containing capsid transcriptase dsDNA and associated enzyme inside enzymes Acquired Associated Smallpox Poliomyelitis immunodeficiency Diseases syndrome (AIDS) 13